It has been long debated on whether the emotion system is subserved by six discrete basic emotion categories (i.e., disgust, anger, fear, happiness, sadness, and surprise). Recent studies showed that perceptual confusion often occurred between fear and surprise and between disgust and anger. arguing for the existence of less than the six basic emotions. However, the neural mechanisms of the confusions are still unknown. To answer this question, we presented subjects with face pictures expressing the six basic emotions and the neutral emotion, while measuring their BOLD signals. We performed multivariate pattern analysis (MVPA) to classify or decode BOLD response patterns between the six basic emotions and the neutral emotion. We found that, in the amygdala, both fear and surprise can be decoded significantly above chance level, and in the superior temporal sulcus (STS), disgust and anger can be decoded significantly above chance level. To further understand the confusion effects, we performed cross-category MVPA, in which a decoder was trained with one emotion (vs. neutral face) and was then applied to decode other emotions (vs. neutral face). The cross-category decoding accuracy was significant between disgust and anger in the STS. However, the decoding accuracy between surprise and fear was not significant in the amygdala. Notably, neither the within- nor cross-category decoding accuracy was significant in face-selective visual areas, including occipital face area (OFA) and fusiform face area (FFA). These findings imply that perceptual confusion between certain emotions (e.g., disgust and anger) is likely to occur at the emotion processing level, rather at the pure visual processing level.